Extrachromosomal DNA from a dicot plant Vigna radiata

Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants

Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It was found in various non-plant organisms from yeast to humans. EccDNA is heterogeneous in size and contains sequences derived primarily from repetitive chromosomal DNA. Here, we report the occurrence of eccDNA in small and large genome plant species, as identified using two-dimensional gel electrophoresis. We show that eccDNA is readily detected in both Arabidopsis thaliana and Brachycome dichromosomatica, reflecting a normal phenomenon that occurs in wild-type plants. The size of plant eccDNA ranges from > 2 kb to < 20 kb, which is similar to the sizes found in other organisms. These DNA molecules correspond to 5S ribosomal DNA (rDNA), non-coding chromosomal high-copy tandem repeats and telomeric DNA of both species. Circular multimers of the repeating unit of 5S rDNA were identified in both species. In addition, similar multimers were also demonstrated with the B. dichromosomatica repetitive element Bdm29. Such circular multimers of tandem repeats were found in animal models, suggesting a common mechanism for eccDNA formation among eukaryotes. This mechanism may involve looping-out via intrachromosomal homologous recombination. The implications of these results on genome plasticity and evolutionary processes are discussed.

Isolation, characterization and sequencing of a novel repetitive DNA from the mung bean Vigna radiata

A family of highly reiterated, small (approx. 300 bp) sequences has been identified in DNA of the mung bean Vigna radiata. The members are extensively interspersed throughout the chromosomes with some clustering. They also occur extrachromosomally. There is no tissue-specificity to the repeat family but it is highly species-specific. The repetitive DNA hybridizes to total RNA as well as to polyadenylated RNA isolated from germinated mung beans. It has analogy with the human AluI family in the mode of isolation, size, genomic distribution, copy number and transcribability though they do not share any sequence homology. A repetitive DNA clone was selected from a shotgun genomic library of mung bean DNA in pBR322. The average copy number of the cloned repeat is estimated to be 8 x 10(4) per haploid genome, and thus constitutes approx. 5% of the total mung bean genome. The genomic organization and transcription of the cloned repeat is reported. Sequencing of the cloned repetitive DNA reveals the presence of the number of direct and inverted repeats and some short palindromic sequences.